Re: AMBER: side chain orientation

From: Esther Brugger <>
Date: Wed, 7 Feb 2007 07:23:55 -0800 (PST)

Dear Fenghui,
 Thanks for your reply.
 In my calculation, there are 2 amino acids in different side of the backbone. Now I am trying to use some figures to show these 2 amino acids in the different direction becasue of the steric hinder effect. For example, if there is no steric hinder effect, they are probably in right side of the bacbone; but now one is in the left side, the other is in the right side. I tried dihedral angle and angle to get it by ptraj program through trajectory file, but the results didn't show what I want. I really wish you may help me figure it out. Thank you very much for your time and help!

Fenghui Fan <> wrote: As for a protein, it should has it PDB file. Then the
coodinates of the two side chains has been decided,
then you can know the orientation. I do not know
whether this is what you want. If not, please tell me
a little in detail on what you really want to get.

Best regards.

Fenghuin Fan

--- Esther Brugger wrote:

> Dear Amber Users,
> Does anyone know which program can be used to
> calculate the orientations of two amino acids which
> are in the different side of backbone of the
> molecule?
> Any advice are appreciated!
> Bests,
> Esther B.
> ---------------------------------
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Esther B.

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Received on Sun Feb 11 2007 - 06:07:07 PST
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